Kästner Johannes, Thiel Walter
Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany.
J Chem Phys. 2006 Jun 21;124(23):234106. doi: 10.1063/1.2206775.
Umbrella sampling simulations, or biased molecular dynamics, can be used to calculate the free-energy change of a chemical reaction. We investigate the sources of different sampling errors and derive approximate expressions for the statistical errors when using harmonic restraints and umbrella integration analysis. This leads to generally applicable rules for the choice of the bias potential and the sampling parameters. Numerical results for simulations on an analytical model potential are presented for validation. While the derivations are based on umbrella integration analysis, the final error estimate is evaluated from the raw simulation data, and it may therefore be generally applicable as indicated by tests using the weighted histogram analysis method.
伞形采样模拟，即有偏分子动力学，可用于计算化学反应的自由能变化。我们研究了不同采样误差的来源，并推导了使用谐振子约束和伞形积分分析时统计误差的近似表达式。这得出了关于偏差势和采样参数选择的普遍适用规则。给出了在解析模型势上进行模拟的数值结果以作验证。虽然推导基于伞形积分分析，但最终误差估计是根据原始模拟数据评估的，因此如使用加权直方图分析方法的测试所示，它可能具有普遍适用性。
